Literature DB >> 26708341

Multiscale simulation of DNA.

Pablo D Dans1, Jürgen Walther1, Hansel Gómez1, Modesto Orozco2.   

Abstract

DNA is not only among the most important molecules in life, but a meeting point for biology, physics and chemistry, being studied by numerous techniques. Theoretical methods can help in gaining a detailed understanding of DNA structure and function, but their practical use is hampered by the multiscale nature of this molecule. In this regard, the study of DNA covers a broad range of different topics, from sub-Angstrom details of the electronic distributions of nucleobases, to the mechanical properties of millimeter-long chromatin fibers. Some of the biological processes involving DNA occur in femtoseconds, while others require years. In this review, we describe the most recent theoretical methods that have been considered to study DNA, from the electron to the chromosome, enriching our knowledge on this fascinating molecule.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 26708341     DOI: 10.1016/j.sbi.2015.11.011

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  42 in total

1.  Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.

Authors:  Mehmet Ali Öztürk; Georgi V Pachov; Rebecca C Wade; Vlad Cojocaru
Journal:  Nucleic Acids Res       Date:  2016-06-07       Impact factor: 16.971

2.  Coarse-grained dynamic RNA titration simulations.

Authors:  S Pasquali; E Frezza; F L Barroso da Silva
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 3.  From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.

Authors:  Matías R Machado; Ari Zeida; Leonardo Darré; Sergio Pantano
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

4.  Martini Coarse-Grained Force Field: Extension to RNA.

Authors:  Jaakko J Uusitalo; Helgi I Ingólfsson; Siewert J Marrink; Ignacio Faustino
Journal:  Biophys J       Date:  2017-06-17       Impact factor: 4.033

Review 5.  Linking Chromatin Fibers to Gene Folding by Hierarchical Looping.

Authors:  Gavin Bascom; Tamar Schlick
Journal:  Biophys J       Date:  2017-01-31       Impact factor: 4.033

6.  How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study.

Authors:  Lihua Bie; Likai Du; Qiaoxia Yuan; Jun Gao
Journal:  J Mol Model       Date:  2018-06-11       Impact factor: 1.810

7.  The "sugar" coarse-grained DNA model.

Authors:  N A Kovaleva; I P Koroleva Kikot; M A Mazo; E A Zubova
Journal:  J Mol Model       Date:  2017-02-09       Impact factor: 1.810

8.  Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.

Authors:  Rommie E Amaro; Adrian J Mulholland
Journal:  Nat Rev Chem       Date:  2018-04-11       Impact factor: 34.035

9.  Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling.

Authors:  Stephanie Portillo-Ledesma; Tamar Schlick
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2019-08-06

10.  cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA.

Authors:  Lennart De Bruin; John H Maddocks
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

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